RosettaAntibody core.pose.util error

[Anonymous]

Hi,

I’m using Rosetta 3.8 on Linux (rosetta_bin_linux_2017.08.59291_bundle; pre-compiled binaries). I’m trying to use the RosettaAntibody3 workflow as documented here, but am running into the following error when I run the sample command (using the sample antibody sequences in antibody_chains.fasta as given in the workflow):

antibody.linuxgccrelease -fasta antibody_chains.fasta

This is the error (with the preceding logging messages):

core.import_pose.import_pose: File '/share/PI/software/rosetta_3.8/rosetta_bin_linux_2017.08.59291_bundle/tools/antibody/antibody_database/pdb2dlf_chothia.pdb' automatically determined to be of type PDB

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 233

core.conformation.Conformation: Found disulfide between residues 23 93

core.conformation.Conformation: current variant for 23 CYS

core.conformation.Conformation: current variant for 93 CYS

core.conformation.Conformation: current variant for 23 CYD

core.conformation.Conformation: current variant for 93 CYD

core.conformation.Conformation: Found disulfide between residues 135 211

core.conformation.Conformation: current variant for 135 CYS

core.conformation.Conformation: current variant for 211 CYS

core.conformation.Conformation: current variant for 135 CYD

core.conformation.Conformation: current variant for 211 CYD

protocols.antibody.grafting: Adjusting frh template sequence [/share/PI/software/rosetta_3.8/rosetta_bin_linux_2017.08.59291_bundle/tools/antibody/antibody_database/pdb1dlf_chothia.pdb]...

protocols.antibody.grafting: By using numbering: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 52B 52C 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 101 102 103 104 105 106 107 108 109 110 111 112

core.conformation.Conformation: Found disulfide between residues 22 98

core.conformation.Conformation: current variant for 22 CYD

core.conformation.Conformation: current variant for 98 CYD

core.conformation.Conformation: current variant for 22 CYD

core.conformation.Conformation: current variant for 98 CYD

protocols.antibody.grafting: Sequence before: EVKLEESGGGLVQPGGSMKLSCATSGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYAESVKGRFTISRDDSKRRVYLQMNTLRAEDTGIYYCTGIYYHYPWFAYWGQGTLVTVS

core.pose.util: Can't find residue type 'UNK' in type set of mode fa_standard

 

This occurs irrespective of what antibody sequences I provide in antibody_chains.fasta. I don’t believe any of the residues in the sequence are non-standard; so am not sure what is going wrong here. Thanks for your help!

 

[Anonymous]

I talked to the main devs of the protocol – adding `-ignore_unrecognized_res` to your cmd-file should fix it.  It is probably the result of an UNK residue in that particular template that the sequence alignment is choosing to use for the modeling. 

[Anonymous]

I am facing with the same problem while trying to repeat RosettaAb protocol using the same fasta file given in the protocol:

 

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 233

core.conformation.Conformation: Found disulfide between residues 23 93

core.conformation.Conformation: current variant for 23 CYS

core.conformation.Conformation: current variant for 93 CYS

core.conformation.Conformation: current variant for 23 CYD

core.conformation.Conformation: current variant for 93 CYD

core.conformation.Conformation: Found disulfide between residues 135 211

core.conformation.Conformation: current variant for 135 CYS

core.conformation.Conformation: 

 

After these messages the run is stopped. I also tried to run RosettaAb using the following comment but the result was the same:

 

antibody.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta | tee grafting.log

 

What should I do next? Thank you for your help.

 

[Author]

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